bims-celmim 2025-11-23 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–11–23
thirty-six papers selected by
Marc Segarra Mondejar, AINA

Elucidating the Localization and Interactome of Mitochondrial Microproteins.
Comparative Evaluation of Hyperpolarized [13C]pyruvate and [13C]lactate for Imaging Neuronal and Glioma Metabolism.
Succinate puts the brakes on de novo purine synthesis.
Alteration of metabolic activity regulates mitochondrial temperature in diagnosis in HepG2 hepatocellular carcinoma cells.
Mitochondrial NAD+ gradient sustained by membrane potential and transport.
TKT drives renal cell carcinoma progression through metabolic reprogramming and synergistic interaction with PKM2.
A new probe illuminates endo-lysosomal Ca2+ measurements: A role for vesicular IP3 receptors?
Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment.
The metabolic engine of cognition: microglia-neuron interactions in health, ageing and disease.
Branched chain amino acids and their aberrant metabolism in cancer.
Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.
How one nutrient controls cell size.
Protocol for investigating mitochondrial structure, function, and metabolism in human cervical cancer cells.
Denoising of fluorescence lifetime imaging data via principal component analysis.
Metabolic Flexibility of Microglia: Energy Substrate Utilization and Impact on Neuronal Metabolism.
Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.
BRSK2 plays a role in autophagy and cancer cell growth and survival under nutrient deprivation stress via the PIK3C3 pathway.
Rac1 promotes proximal tubule kidney repair by coupling the actin cytoskeleton to mitochondrial function.
Analysis of Cellular Metabolism Using Flow Cytometry.
Parameterization of cell-free systems with time-series data using KETCHUP.
Quantifying Mitochondrial Metabolism and Metabolic Fluxes in Soft Agar Cultures.
Investigating the effects of membrane curvature inducing proteins on lipid droplets in Saccharomyces cerevisiae.
Atg16l1 promotes lung transplant tolerance by regulating glycolysis in macrophages.
SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
Mechanochemical mechanism underlying intercellular Ca2+ wave propagation and its crucial role in apoptotic cell extrusion.
An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice.
Longitudinal transformation of mitochondrial metabolism during neurogenesis.
Traumatic brain injury exacerbates mitochondrial dysfunction in APP/PS1 knock-in mice through time-dependent pathways.
Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.
Amyloid-beta glycation induces neuronal mitochondrial dysfunction and Alzheimer's pathogenesis via VDAC1-dependent mtDNA efflux.
Structures of human organellar SPFH protein complexes.
Retrograde mitochondrial transport regulates mitochondrial biogenesis in zebrafish neurons.
Stable intracranial imaging of dura mater-engrafted pancreatic islet cells in awake mice.
FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.
Resveratrol delays senescence of human dental pulp stem cells via activating the SIRT1-mitochondrial autophagy.
Caloric restriction enhances inheritance of wild-type mitochondrial DNA in Saccharomyces cerevisiae.

Methods Mol Biol. 2026 ;2992 213-228

Elucidating the Localization and Interactome of Mitochondrial Microproteins.

Jiemin Nah, Pooja Sridharan, Lena Ho.

  A large number of novel microproteins discovered to date are nuclear encoded, mitochondrial proteins, pointing to their widespread roles in metabolic regulation. In this chapter, we provide a workflow of how to verify if a candidate microprotein is localized to the mitochondria, its submitochondrial localization (i.e., outer, inner membrane, or matrix) and how to determine its interactome in order to elucidate its molecular function.

Keywords:  Microproteins; Mitochondria; OXPHOS

DOI:  https://doi.org/10.1007/978-1-0716-5013-4_15
ACS Sens. 2025 Nov 21.

Comparative Evaluation of Hyperpolarized [13C]pyruvate and [13C]lactate for Imaging Neuronal and Glioma Metabolism.

Jun Chen, Maheen Zaidi, Jaideep Chaudhary, Zohreh Erfani, Sarah Al Nemri, Erik J Plautz, Xiaodong Wen, Erin H Seeley, Brenda L Bartnik-Olson, Ian R Corbin, Jae Mo Park.

  Glucose and lactate are primary substrates in cerebral energy metabolism. Hyperpolarized [1-13C]pyruvate has become a powerful imaging agent for metabolic neuroimaging due to its central role in glucose and lactate metabolism, ability to cross the blood-brain barrier, and translational utility in neurological disorders. In particular, [1-13C]pyruvate enables an assessment of mitochondrial metabolism in the cerebral cortex through its conversion to [13C]bicarbonate. While it is not yet confirmed that production of [13C]bicarbonate primarily reflects neuronal metabolism, the higher affinity of neuronal transporters for lactate over pyruvate has motivated interest in hyperpolarized lactate as a more physiologic probe of neuronal metabolism. Here, we identify the predominant cellular source of [13C]bicarbonate and evaluate [1-13C]lactate as an imaging agent for neuronal metabolic imaging. Ex vivo NMR and mass spectrometry imaging of brain tissue collected after bolus injection of [U-13C3]pyruvate revealed that pyruvate dehydrogenase dominates pyruvate carboxylase in the cortex, supporting the neuronal origin of [13C]bicarbonate production. Although the bicarbonate fraction among the total 13C products in vivo was higher following hyperpolarized [1-13C]lactate injection, the signal sensitivity was markedly reduced due to lactate's shorter T1 and larger endogenous pool. Isotopomer analysis of brain tissue harvested 2 min after injection of [U-13C3]pyruvate or [U-13C3]lactate showed comparable labeling of mitochondrial intermediates. In glioma-bearing rats, in vivo imaging revealed an elevated pyruvate-to-lactate ratio within the tumor, highlighting altered redox and transport dynamics in malignancy. These findings demonstrate that both hyperpolarized [1-13C]pyruvate and [1-13C]lactate can effectively probe neuronal and glioma metabolism, although pyruvate outperforms lactate in detecting pyruvate dehydrogenase flux.

Keywords:  hyperpolarization; lactate metabolism; mass spectrometry imaging; neuroimaging; neuron

DOI:  https://doi.org/10.1021/acssensors.5c03203
Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00861-5. [Epub ahead of print]85(22): 4109-4110

Succinate puts the brakes on de novo purine synthesis.

Timothy C Kenny, Kıvanç Birsoy.

In this issue of Molecular Cell, Nengroo et al.1 report that the tricarboxylic acid (TCA) cycle enzyme succinate dehydrogenase (SDH) is essential for de novo purine synthesis, revealing a previously unrecognized metabolic dependency in cancer that can be leveraged therapeutically.

DOI: https://doi.org/10.1016/j.molcel.2025.10.020
Sci Rep. 2025 Nov 21. 15(1): 41155

Alteration of metabolic activity regulates mitochondrial temperature in diagnosis in HepG2 hepatocellular carcinoma cells.

Ola A Gaser, Mohamed A Nasr, Alaa E Hussein, Radwa Ayman Salah, Shams M Saad, Seif Ehab, Nourhan M Aboomar, Ahmed O Elmehrath, Ayman Salah, Young-Tae Chang, Mal Hedrick, Lázaro A M Castanedo, Peyman Fahimi, Chérif F Matta, Nagwa El-Badri.

  Oxidative phosphorylation (OXPHOS) is a key player in mitochondrial bioenergetic functions. In hepatocellular carcinoma (HCC), OXPHOS slows down or switches to glycolysis via what is known as the Warburg effect. The altered respiration in cancer was reported to affect mitochondrial temperature. We investigated the impact of the metabolic switch on the mitochondrial temperature in HepG2 HCC cell line. Metformin (N, N-dimethylbiguanide) treatment was used to suppress glycolysis to emulate lower metabolically active cells (Met-HepG2). The mitochondrial temperature was assessed using mito-thermo yellow (MTY) absorbing mitochondrial radiant heat. Mito-tracker green (MTG) fluorescent dye was used to confirm mitochondrial localization. Our data showed lower MTY dye intensity in the Met-HepG2 treated group, indicating a significant increase in mitochondrial temperature compared to untreated HepG2 cells (NT-HepG2). Genotypic analysis of the metabolic respiration gene expression showed significant down-regulation in glycolytic genes (ERR-gamma, HK2, PGK, ALDOC, TPI1, IDH1, and PKM2) in the Met-HepG2 cells compared to the NT-HepG2 cells. OXPHOS as evidenced by ATP, ROS, and NADPH production was significantly up-regulated in the Met-HepG2 group compared to the NT-HepG2 group. Transmission electron microscopy showed fewer mitochondria with swollen elongated appearance, as a marker for activated OXPHOS in the Met-HepG2 group. These data show a correlation between HepG2 altered metabolism and mitochondrial temperature and suggest that less metabolically active HepG2 cells are correlated with higher mitochondrial temperature, providing evidence for a possible role of mitochondrial temperature in diagnosis of HCC.

Keywords:  Cancer; Hepatocellular carcinoma (HCC); Mito thermo yellow (MTY); Mitochondrial bioenergetics; Mitochondrial temperature

DOI:  https://doi.org/10.1038/s41598-025-02807-0
Sci Adv. 2025 Nov 21. 11(47): eaea7460

Mitochondrial NAD+ gradient sustained by membrane potential and transport.

Shivansh Goyal, Scott N Lyons, Xiaolu A Cambronne.

SLC25A51 is required for the replenishment of free nicotinamide adenine dinucleotide (oxidized form) (NAD+) into mammalian mitochondria. However, it is not known how SLC25A51 imports this anionic molecule to sustain elevated NAD+ concentrations in the matrix. Understanding this would reveal regulatory mechanisms used to maintain critical bioenergetic gradients for cellular respiration, oxidative mitochondrial reactions, and mitochondrial adenosine triphosphate (ATP) production. In this work, mutational analyses and localized NAD+ biosensors revealed that the mitochondrial membrane potential (ΔΨm) works in concert with charged residues in the carrier's inner pore to enable sustained import of NAD+ against its electrochemical gradient into the matrix. Dissipation of the ΔΨm or mutation of select residues in SLC25A51 led to equilibration of NAD+ from the matrix. Corroborating data were obtained with the structurally distinct mitochondrial NAD+ carrier from Saccharomyces cerevisiae (ScNdt1p) and mitochondrial ATP transport suggesting a shared mechanism of charge compensation and electrogenic transport in these mitochondrial carrier family members.

DOI: https://doi.org/10.1126/sciadv.aea7460
Cell Death Discov. 2025 Nov 18. 11(1): 537

TKT drives renal cell carcinoma progression through metabolic reprogramming and synergistic interaction with PKM2.

Qianqing Wang, Anqun Tang, Qingxin Zhuang, Haifeng Xu, Shiping Xu, Jing Zhang, Yao Wang, Liantao Li, Sufang Chu, Yan Wang, Jin Bai, Minle Li, Rui Zhang.

Renal cell carcinoma (RCC) undergoes profound metabolic reprogramming to fuel its aggressive progression and metastatic dissemination. While transketolase (TKT), a central metabolic enzyme, has been shown to exert dichotomous roles as either oncogenic or tumor-suppressive factors across different malignancies, its functional significance in RCC pathogenesis remains inadequately defined. In this study, we demonstrate that TKT promotes glucose metabolism in RCC by enhancing glycolysis, thereby supporting tumor progression. TKT expression is significantly elevated in RCC tissues and correlates with poor patient prognosis. Mechanistically, we uncovered a novel functional axis between TKT and the glycolytic gatekeeper pyruvate kinase M2 (PKM2), where their coordinated action drives metastatic progression and metabolic adaptation in RCC. Knockdown of PKM2 significantly impaired the TKT-mediated increases in glycolysis, cell proliferation, and invasive potential. Taken together, our findings highlight TKT as a pivotal regulator of metabolic reprogramming in RCC and suggest its potential as a therapeutic target for the treatment of this malignancy.

DOI: https://doi.org/10.1038/s41420-025-02837-7
J Cell Biol. 2025 Dec 01. pii: e202511020. [Epub ahead of print]224(12):

A new probe illuminates endo-lysosomal Ca2+ measurements: A role for vesicular IP3 receptors?

Anthony J Morgan.

In this issue, Calvo et al. (https://doi.org/10.1083/jcb.202410094) report a new bioluminescent Ca2+ probe (ELGA) targeted to acidic endo-lysosomes (ELs) to permit selective and dynamic recording of endo-lysosomal Ca2+ uptake and release. Ca2+ was not only released by canonical EL channels but, surprisingly, by IP3 receptors.

DOI: https://doi.org/10.1083/jcb.202511020
bioRxiv. 2025 Oct 04. pii: 2025.10.02.680066. [Epub ahead of print]

Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment.

Brian Kelly, Chia-Hua Wu, Kaan I Eskut, Elizabeth McCauley, Sajina Dhungel, Samantha Pavlecic, Grace Bieghler, Jelena Perovanovic, Dean Tantin, Jakub Famulski, Jeramiah Smith, Chintan Kikani.

Myogenic commitment is a decisive and irreversible step in skeletal muscle regeneration, necessitating proliferating myoblasts to integrate metabolic cues with nuclear transcriptional programs. Among amino acids, glutamine is uniquely positioned to influence this transition by coupling energy production to macromolecule biosynthesis and epigenetic regulation. We reasoned that myoblasts must sense glutamine availability to ensure orderly progression toward commitment, and we tested this by examining the molecular consequences of acute glutamine withdrawal. We find that continued glutamine oxidation is required to sustain glycolysis, maintain mitochondrial fission, and preserve a redox balance that supports progression towards myogenic commitment. In its absence, myoblasts undergo a reductive shift, characterized by mitochondrial elongation, membrane depolarization, and suppression of glycolysis, ultimately leading to growth arrest. Transcriptomic profiling reveals reduced MyoD and MKi67 , accompanied by increased Sprouty1 levels, defining a reversible non-proliferative state that resembles but is distinct from quiescent and reserve cells. We term this state Poised Metabolic Arrest (PMA), a cellular response to glutamine limitation during myogenic progression. Mechanistically, PMA is driven by Nrf2-dependent increased glutathione (GSH) biosynthesis and upregulation of mitochondrial GSH carrier Slc25a39 when glutamine is limited. Depleting mitochondrial glutathione or silencing Slc25a39 forces exit from PMA. However, this premature exit compromises subsequent differentiation potential, indicating PMA serves to preserve differentiation competence when glutamine is limited. Consistent with this, both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt regeneration in vivo. Together, these data suggest that a reciprocal Slc25a39-Nrf2 redox axis functions as a nutrient-dependent checkpoint, coupling glutamine availability to mitochondrial remodeling and metabolic reprogramming, necessary to establish irreversible myogenic commitment.

DOI: https://doi.org/10.1101/2025.10.02.680066
Nat Metab. 2025 Nov 21.

The metabolic engine of cognition: microglia-neuron interactions in health, ageing and disease.

Evridiki Asimakidou, Stefano Pluchino, Bianca Ambrogina Silva, Luca Peruzzotti-Jametti.

Cognitive impairment is associated with perturbations of fine-tuned neuroimmune interactions. At the molecular level, alterations in cellular metabolism can compromise brain function, driving structural damage and cognitive deficits. In this Review, we focus on the bidirectional interactions between microglia, the brain-resident immune cells and neurons to dissect the metabolic determinants of brain resilience and cognition. We first outline these metabolic pathways during development and adult life. Then, we delineate how these processes are perturbed in ageing, as well as in metabolic, neuroinflammatory and neurodegenerative disorders. By doing so, we provide a mechanistic understanding of the metabolic pathways relevant to cognitive function in health and disease, thus paving the way for novel therapeutic targets based on the emerging field of neuroimmunometabolism.

DOI: https://doi.org/10.1038/s42255-025-01409-4
Trends Cancer. 2025 Nov 18. pii: S2405-8033(25)00255-9. [Epub ahead of print]

Branched chain amino acids and their aberrant metabolism in cancer.

Morgan L Brown, Xuanyan Cai, M Celeste Simon.

  Cancer cells require sufficient nutrients to support biomass generation, rapid proliferation, and survival. Thus, extensive reprogramming of amino acid metabolism is necessary for tumor initiation and progression under strenuous conditions. One metabolic pathway that has garnered attention is branched chain amino acid (BCAA) catabolism, a pathway that is highly altered across malignancies. This review examines current insights into how circulating BCAAs and their aberrant catabolic enzymes impact both cancer cells and the surrounding tumor microenvironment.

Keywords:  branched chain amino acids; cancer metabolism; nutrient supplementation; tumor microenvironment

DOI:  https://doi.org/10.1016/j.trecan.2025.10.004
Cancer Res. 2025 Nov 17.

Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.

Maria Dubisova, Klara Bohacova, Zuzana Nahacka, Daniel Kraus, Jaromir Novak, Sarka Dvorakova, Petra Brisudova, Natalie Danesova, Saba Selvi, Mariia Hrysiuk, Berwini B Endaya, Panagiotis Botsios, Dan-Diem Thi Le, Monika Novotna, Sona Vodenkova, Jaroslav Truksa, Karel Chalupsky, Krystof Klima, Jan Prochazka, Radislav Sedlacek, Francesco Mengarelli, Patrick Orlando, Luca Tiano, Stepana Boukalova, Michael V Berridge, Renata Zobalova, Jiri Neuzil.

Cancer cells with severe defects in mitochondrial DNA (mtDNA) can import mitochondria via horizontal mitochondrial transfer (HMT) to restore respiration. Mitochondrial respiration is necessary for the activity of dihydroorotate dehydrogenase (DHODH), an enzyme of the inner mitochondrial membrane that catalyzes the fourth step of de novo pyrimidine synthesis. Here, we investigated the role of de novo synthesis of pyrimidines in driving tumor growth in mtDNA-deficient (ρ0) cells. While ρ0 cells grafted in mice readily acquired mtDNA, this process was delayed in cells transfected with alternative oxidase (AOX), which combines the functions of mitochondrial respiratory complexes III and IV. The ρ0 AOX cells were glycolytic but maintained normal DHODH activity and pyrimidine production. Deletion of DHODH in a panel of tumor cells completely blocked or delayed tumor growth. The grafted ρ0 cells rapidly recruited tumor-promoting/stabilizing cells of the innate immune system, including pro-tumor M2 macrophages, neutrophils, eosinophils, and mesenchymal stromal cells (MSCs). The ρ0 cells recruited MSCs early after grafting, which were potential mitochondrial donors. Grafting MSCs together with ρ0 cancer cells into mice resulted in mitochondrial transfer from MSCs to cancer cells. Overall, these findings indicate that cancer cells with compromised mitochondrial function readily acquire mtDNA from other cells in the tumor microenvironment to restore DHODH-dependent respiration and de novo pyrimidine synthesis. The inhibition of tumor growth induced by blocking DHODH supports targeting pyrimidine synthesis as a potential widely applicable therapeutic approach.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0737
Elife. 2025 Nov 19. pii: e109482. [Epub ahead of print]14

How one nutrient controls cell size.

Angela Montero, Lydia W S Finley.

  The metabolic fate of a nutrient called pyruvate determines how big cells become.

Keywords:  D. melanogaster; biochemistry; cell biology; cell growth; chemical biology; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation

DOI:  https://doi.org/10.7554/eLife.109482
STAR Protoc. 2025 Nov 19. pii: S2666-1667(25)00608-2. [Epub ahead of print]6(4): 104202

Protocol for investigating mitochondrial structure, function, and metabolism in human cervical cancer cells.

Sachin Shetty, Shama Prasada Kabekkodu.

  Mitochondria regulate a variety of biological activities, including metabolism, oxidative stress, and cell death. Here, we present a protocol for the investigation of mitochondrial structure, function, and metabolism in human cervical cancer cells. We describe steps for staining and visualizing mitochondria using confocal microscopy to assess morphology, mass, membrane potential, calcium, reactive oxygen species (ROS), and lipid droplet accumulation. We then detail procedures for isolating mitochondria and performing metabolomic analysis of mitochondrial metabolites via mass spectrometry. For complete details on the use and execution of this protocol, please refer to Adiga et al.1.

Keywords:  cancer; cell biology; molecular biology

DOI:  https://doi.org/10.1016/j.xpro.2025.104202
Sci Rep. 2025 Nov 17. 15(1): 40258

Denoising of fluorescence lifetime imaging data via principal component analysis.

Soheil Soltani, Jack G Paulson, Emma J Fong, Shannon M Mumenthaler, Andrea M Armani.

  Fluorescence Lifetime Imaging Microscopy (FLIM) quantifies autofluorescence lifetime to assess cellular metabolism, therapeutic efficacy, and disease progression. These dynamic and heterogeneous processes complicate signal analysis. Fit-free analysis methods such as phasor analysis are increasingly used due to limitations of fit-based approaches. However, incorporating photon-counting shot noise often leads to moderate-to-high uncertainty in detecting subtle changes. Common noise-reduction strategies can introduce errors and cause data loss. We developed noise-corrected principal component analysis (NC-PCA), which selectively identifies and removes noise to isolate the signal of interest. We validated NC-PCA by analyzing FLIM images of patient-derived colorectal cancer organoids treated with several therapeutics. First, we show NC-PCA decreases uncertainty by up to 5.5-fold compared to conventional analysis and reduces data loss over 50-fold. Then, using a merged dataset, NC-PCA reveals multiple metabolic states. Overall, NC-PCA offers a powerful, generalizable tool to enhance FLIM analysis and improve detection of biologically relevant metabolic changes.

Keywords:  Adaptive noise removal; Data retention; Denoising; FLIM; FLIM analysis; Fluorescence lifetime imaging microscopy; Metabolic imaging; Organoid imaging; Principal component analysis

DOI:  https://doi.org/10.1038/s41598-025-24022-7
J Neurochem. 2025 Nov;169(11): e70304

Metabolic Flexibility of Microglia: Energy Substrate Utilization and Impact on Neuronal Metabolism.

Emil W Westi, Rebecca Birch Carlsen, Jens Velde Andersen, Zeliha Kilic, Dana Alnajar, Nadia K Holmgaard, Belén García Sintes, Agustin Cota-Coronado, Sonia Sanz Muñoz, Céline Galvagnion, Blanca I Aldana.

  Microglia, the main resident immune cells of the brain, play critical roles in maintaining neuronal function and homeostasis. Microglia's metabolic flexibility enables rapid adaptation to environmental changes, yet the full extent of their metabolic capabilities and influence on neuronal metabolism remains unclear. While microglia predominantly rely on glucose oxidative metabolism under homeostatic conditions, they shift towards glycolysis upon proinflammatory activation. In this study, we investigated microglial metabolism and its impact on neuronal metabolic homeostasis using isotope tracing with stable carbon 13C-enriched substrates and gas chromatography-mass spectrometry (GC-MS) analysis. Primary microglia were incubated with 13C-labeled glucose, glutamine, or GABA in the presence or absence of lipopolysaccharide (LPS) to assess metabolic adaptations upon an inflammatory challenge. Additionally, neurons co-cultured with quiescent or activated microglia (either with LPS or amyloid-β) were incubated with 13C-enriched glucose to examine microglia-neuron metabolic interactions. Our findings confirm that microglia readily metabolize glucose and glutamine, with LPS stimulation slightly changing the glycolytic activity, as indicated by subtle changes in extracellular lactate. Importantly, we demonstrate for the first time that microglia take up and metabolize the inhibitory neurotransmitter GABA, suggesting a novel metabolic function. Furthermore, microglial presence directly influences neuronal metabolism and neurotransmitter homeostasis, highlighting a previously unrecognized aspect of neuron-microglia metabolic crosstalk. Collectively, these findings provide new insights into microglial metabolism and its role in neuronal function, with implications for neuroinflammatory and neurodegenerative diseases in which microglial metabolism is dysregulated.

Keywords:  GABA metabolism; amyloid‐beta; glutamine; metabolic flexibility; neuroimmune interactions; neurons

DOI:  https://doi.org/10.1111/jnc.70304
bioRxiv. 2025 Sep 29. pii: 2025.09.28.674326. [Epub ahead of print]

Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.

Vasileios Chortis, Kleiton Silva Borges, Cong-Hui Yao, Claudio Ribeiro, Luis Fernando Nagano, Mesut Berber, Alessandro Prete, Lukáš Najdekr, Michail E Klontzas, Andris Jankevics, Pedro Vendramini, Jean Lucas Kremer, Liam Kelley, Sathuwarman Raveenthiraraj, Stylianos Tsagarakis, Magdalena Macech, Ivana D Pupovac, Thomas G Papathomas, Betul Haykir, Catherine Winder, Marcus Quinkler, M Conall Dennedy, Grethe Å Ueland, Felix Beuschlein, Antoine Tabarin, Martin Fassnacht, Angela E Taylor, Darko Kastelan, Urszula Ambroziak, Dimitra A Vassiliadi, Katja Kiseljak-Vassiliades, Irina Bancos, Diana L Carlone, Warwick B Dunn, Wiebke Arlt, Marcia C Haigis, David T Breault.

Dysregulation of cellular metabolism is a hallmark of cancer, which remains poorly understood in adrenocortical carcinoma (ACC). Here, we dissected ACC metabolism by integrating transcriptional profiling from human and mouse ACC, targeted tissue metabolomics from a mouse ACC model, and untargeted serum metabolomics from a large patient cohort, providing cross-species validation of metabolic rewiring in ACC. This study revealed global metabolic dysregulation, involving glutamine-dependent pathways such as non-essential amino-acid and hexosamine biosynthesis, nucleotide metabolism, and glutathione biosynthesis, suggesting glutamine catabolism is a critical metabolic vulnerability in ACC. Treatment with glutamine antagonists 6-Diazo-5-Oxo-L-Norleucine (DON) and JHU-083 elicited robust anti-tumor responses. Mechanistic studies revealed DON's anti-tumor effect was primarily driven by selective inhibition of glutamine-fueled de novo nucleotide biosynthesis. Additionally, DON led to DNA damage, which yielded potent synergism with inhibition of the DNA damage response pathway. Collectively, this work highlights glutamine metabolism as a central metabolic dependency and therapeutic target in ACC.

DOI: https://doi.org/10.1101/2025.09.28.674326
Sci Rep. 2025 Nov 19. 15(1): 40651

BRSK2 plays a role in autophagy and cancer cell growth and survival under nutrient deprivation stress via the PIK3C3 pathway.

Aparna Maiti, Alison D Axtman, Rongrong Wu, Lydia J B Redman, Kazuaki Takabe, Aimee B Stablewski, Li Yan, Michael J Ciesielski, Jianmin Zhang, Sharon S Evans, Pawel Kalinski, Nitai C Hait.

  Macroautophagy/autophagy is a stress-responsive lysosomal catabolic pathway that promotes cellular homeostasis and tumor cell survival, but its role in breast cancer progression and metastasis remains unclear. Here, we show that a brain-specific serine/threonine protein kinase, BRSK2, a marker of aggressive metastatic disease in breast cancer patients, is crucial in regulating autophagy. BRSK2 is overexpressed in aggressive cancer and is associated with reduced disease-specific survival. BRSK2 also regulates basal autophagy and activates AKT, STAT3, and NF-κB-mediated cancer cell survival pathways. In addition, BRSK2 overexpression increases the levels of inflammatory cytokines and chemokines in breast cancer cells. Downregulation of BRSK2 using specific siRNAs or the BRSK2 kinase small-molecule inhibitor GW296115 markedly reduced nutrient-deprivation stress-mediated autophagy, cell growth, and metastatic potential, and enhanced breast cancer cell apoptosis. Endogenous BRSK2 is associated with the Vps34-class III PI3K-Beclin-1-ATG14 autophagy signaling complexes that could protect cancer cells from nutrient-deprivation stress. Our findings demonstrate the key role of the BRSK2-mediated protective autophagy and cell growth and survival under nutrient deprivation stress via survival signals, e.g., PI3K/AKT or STAT3-NF-kB, in aggressive breast cancer cells.

Keywords:  Autophagy; BRSK2; Breast cancer; Cell survival; Nutrient-deprivation stress

DOI:  https://doi.org/10.1038/s41598-025-24354-4
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2504565122

Rac1 promotes proximal tubule kidney repair by coupling the actin cytoskeleton to mitochondrial function.

Olga M Viquez, Meiling Melzer, Shensen Li, Matthew Tantengco, Xinyu Dong, Eric Sha, Jeffery Huang, Evan S Krystofiak, Rachel C Hart, Wentian Luo, Christian Warren, Al-Borhan Bayazid, Richard Zhang, Ryoichi Bessho, Volker H Haase, Cord Brakebusch, Takanari Inoue, Craig Brooks, Matthew H Wilson, Andrew S Terker, Juan P Arroyo, Ambra Pozzi, Roy Zent, Fabian Bock.

  The kidney proximal tubule (PT) is a specialized polarized epithelium that functions as a high capacity resorptive machine. PT cells are exquisitely sensitive to ischemia due to their high metabolic rate. The small GTPase Rac1 regulates epithelial function by promoting polarity through its effects on the actin cytoskeleton. We show that Rac1, in the setting of the recovery of the PT from ischemic injury, plays a critical role in reconstituting cellular bioenergetics by promoting actin cytoskeleton formation around damaged mitochondria. This mechanism removes damaged mitochondria through mitophagy and preserves PT metabolic capacity and reabsorption function. Loss of Rac1 causes intracellular lipid accumulation, energy depletion, and PT cell atrophy. Thus, Rac1 promotes the repair of PT cells by enhancing mitochondrial bioenergetics, rather than by regulating cell polarity via a mechanism that links the actin cytoskeleton to metabolic demands and cell morphology.

Keywords:  actin cytoskeleton; kidney repair; mitochondria

DOI:  https://doi.org/10.1073/pnas.2504565122
Methods Mol Biol. 2026 ;2990 119-125

Analysis of Cellular Metabolism Using Flow Cytometry.

Christos Aronis, Matteo Villa.

  The understanding that cellular metabolism underlines the differentiation, activation, and function of immune cells has opened new avenues to modulate immunity. Here, we describe a method to analyze cellular metabolism using the quintessential immunological technique: flow cytometry. We analyze single cell suspensions, by combining the staining of surface immune cell markers and nutrient transporters, with the staining using metabolic dyes, to readout surrogates of metabolic pathway utilization with cell subset resolution.

Keywords:  Cellular metabolism; Flow cytometry; Metabolic dyes; Single cell analysis; Surface nutrient transporters

DOI:  https://doi.org/10.1007/978-1-0716-4997-8_10
PLoS Comput Biol. 2025 Nov;21(11): e1013724

Parameterization of cell-free systems with time-series data using KETCHUP.

Mengqi Hu, Syed Bilal Jilani, Daniel G Olson, Costas D Maranas.

Kinetic models mechanistically link enzyme levels, metabolite concentrations, and allosteric regulation to metabolic reaction fluxes. This coupling allows for the quantitative elucidation of the dynamics of the evolution of metabolite concentrations and metabolic fluxes as a function of time. So far, most large-scale kinetic model parameterizations are carried out using mostly steady-state flux measurements supplemented with metabolomics and/or proteomics data when available. Even though the parameterized kinetic model can trace a temporal evolution of the system, lack of anchoring to temporal data reduces confidence in the dynamics predictions. Notably, the simulation of enzymatic cascade reactions requires a full description of the dynamics of the system as a steady-state is not applicable given that all measured metabolite concentrations vary with time. Here we describe how kinetic parameters fitted to the dynamics of single-enzyme assays remain accurate for the simulation of multi-enzyme cell-free systems. Herein, we demonstrate two extensions for the Kinetic Estimation Tool Capturing Heterogeneous datasets Using Pyomo (KETCHUP) software tool for parameterizing a kinetic model of the cell-free kinetics of formate dehydrogenase (FDH) and 2,3-butanediol dehydrogenase (BDH) through the use of time-course data across various initial conditions. An implemented extension of KETCHUP allowing for the reconciliation of measurement time-lag errors present in datasets was used to parameterize kinetic models using multiple datasets. By combining the kinetic parameters identified by the FDH and BDH assays, accurate simulation of the binary FDH-BDH system was achieved.

DOI: https://doi.org/10.1371/journal.pcbi.1013724
Methods Mol Biol. 2026 ;2990 127-143

Quantifying Mitochondrial Metabolism and Metabolic Fluxes in Soft Agar Cultures.

Birte Dowerg, Fangfang Chen, Thekla Cordes.

  Anchorage-independent cultures provide insights into cell proliferation, differentiation, and tumorigenesis beyond traditional two-dimensional models by mimicking parts of the extracellular matrix (ECM). The soft agar colony formation assay enables cells to proliferate in a three-dimensional manner resulting in metabolic phenotypes that are distinct from traditional monolayer cultures. Here, we established a soft agar colony formation assay with subsequent cell isolation to analyze mitochondrial metabolism, metabolic fluxes, morphology, and gene expression within the same sample. We applied mass spectrometry and tracing approaches to decipher carbon utilization for tricarboxylic acid (TCA) cycle metabolism. We also quantified the alteration of immune-related genes in response to inflammatory stimuli in soft agar cultures that might be relevant to autoimmune diseases, which are frequently associated with inflammatory environments and may contribute insights into chronic inflammation and immune cell survival that parallel tumorigenic processes. Our methodology offers a robust model to better understand cell metabolism and function of anchorage-independent cultures that may contribute to the development of new treatment strategies.

Keywords:  Anchorage-independent cultures; Extracellular matrix; Mass spectrometry; Metabolic flux; Metabolism; Metabolite extraction; Mitochondria; Soft agar; Stable isotope tracer

DOI:  https://doi.org/10.1007/978-1-0716-4997-8_11
Mol Biol Rep. 2025 Nov 19. 53(1): 102

Investigating the effects of membrane curvature inducing proteins on lipid droplets in Saccharomyces cerevisiae.

Laura R K Niemelä, Isabell Tunn, Alexander D Frey.

   BACKGROUND: Reticulons (Rtn1p, Rtn2p) and Yop1p are proteins shaping the endoplasmic reticulum (ER) membrane curvature their function being to a large degree responsible for molding the membrane curvature in the tubular ER area. Lipid biosynthesis mainly takes place in the tubular parts of the ER and lipid droplets are formed in the tubular ER membrane. Nucleation constitutes the rate-limiting step in lipid droplet formation and is modulated by membrane curvature; specifically increasing membrane curvature lowers the activation energy required for lipid lens nucleation. The aim of this work was to investigate the effects, modifying the ER membrane curvature would have on lipid droplets in Saccharomyces cerevisiae.
METHODS AND RESULTS: We created and screened strains overexpressing different combinations of the membrane curvature inducing genes RTN1, RTN2 and YOP1 and additionally the gene inducing ER membrane expansion, DGK1, in four different genetic strain backgrounds. We examined the strains by microscopy and quantified lipid composition by gas chromatography-mass spectrometry. We found that overexpressing membrane curvature inducing proteins decreases the size of the lipid droplets. A reduction in lipid droplet size was accompanied by an apparent increase in their number. We observed that the change in cell size seemed to be partially connected to the strain background. We also noticed altered lipid composition which was linked to the strain backgrounds.
CONCLUSIONS: Overexpression of curvature inducing proteins affected lipid droplet size and number, presumably by affecting nucleation. However, the morphological changes of lipid droplets were not accompanied by increased lipid production. Our findings provide a basis for future research on how ER structure modifications influence the lipid droplet dynamics in S. cerevisiae.

Keywords:   Saccharomyces cerevisiae ; Endoplasmic reticulum; Lipid droplets; Membrane curvature; Reticulons

DOI:  https://doi.org/10.1007/s11033-025-11261-0
bioRxiv. 2025 Oct 04. pii: 2025.10.02.679826. [Epub ahead of print]

Atg16l1 promotes lung transplant tolerance by regulating glycolysis in macrophages.

Marlene Cano, Fuyi Liao, Dequan Zhou, Catherine Chen, Zhiyi Liu, Jihong Zhu, Cory Bernadt, Ricky Ebenezer, Victoria Davis, Katy N Pugh, Yan Tao, Laneshia K Tague, Howard J Huang, Derek E Byers, Ramsey R Hachem, Steven L Brody, Alexander S Krupnick, Daniel Kreisel, Andrew E Gelman.

Lung transplant survival is limited by the development of chronic lung allograft dysfunction (CLAD), a type of graft rejection that lacks effective treatments. Autophagy plays a crucial role in maintaining cellular homeostasis. In a single-nucleotide polymorphism screen, we found that lung recipients with two copies of a common hypofunctional genetic variant of autophagy-related 16-like 1 rs2241880 ( ATG16L1 T300A/T300A ), known to deplete this protein from macrophages, were more likely to develop early CLAD. To understand this, we used a mouse orthotopic lung transplant model. Recipients encoding myeloid cell-specific deletion of Atg16l1 ( Atg16l1 Δ/Δ ) or who harbor an engineered orthologous mutation ( Atg16l1 T316A/T316A ) showed similar susceptibility to CLAD. Transcript profiling and mitochondrial tracking studies indicated that increased mitochondrial damage and decreased autophagic removal of mitochondria in Atg16l1-deficient macrophages were associated with heightened activation of the hypoxia-inducible factor 1α (Hif1α) pathway and accumulation of glycolytic transcripts. Metabolic analysis revealed reduced oxidative phosphorylation, increased glycolytic activity, and higher IL-1β expression in Atg16l1-deficient macrophages. Notably, the development of CLAD in Atg16l1 Δ/Δ lung recipients could be significantly prevented by additionally deleting Hif1α in myeloid cells or by treating with the glycolysis inhibitor 2-deoxyglucose. Our results show how a common autophagy-related genetic variant disrupts macrophage metabolism and impairs lung transplant tolerance, pointing toward potential therapeutic strategies to combat CLAD.

DOI: https://doi.org/10.1101/2025.10.02.679826
Nat Commun. 2025 Nov 20. 16(1): 10198

SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.

Cecilia Colson, Yujue Wang, James Atherton, Nisha Rani Dahiya, Davood Kharaghani, Xiaoyang Su.

Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We develop a metabolomic-transcriptomic association analysis, and we find that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrate that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the peroxisome membrane to facilitate GABA production. Taken together, our results reveal a biochemical mechanism where SLC45A4 controls GABA production.

DOI: https://doi.org/10.1038/s41467-025-62721-x
Nat Commun. 2025 Nov 17. 16(1): 9887

Mechanochemical mechanism underlying intercellular Ca2+ wave propagation and its crucial role in apoptotic cell extrusion.

Sohei Yamada, Ryohei Yasukuni, Yasumasa Bessho, Yasuyuki Fujita, Yoichiroh Hosokawa, Takaaki Matsui.

Calcium (Ca2+) wave propagation plays a crucial role in intercellular communication. Elevation of cytosolic Ca2+ (Ca2+ transient) in a single cell is attributed to various Ca2+ channels present in the plasma membrane and endoplasmic reticulum, whereas gap junctions contribute to propagation of Ca2+ waves between cells. However, we found that Ca2+ waves propagate without gap junctions during apoptotic cell extrusion (ACE). Mechanistically, we identified that a chain reaction of mechano-signal transduction from proximal to distal cells through the mechanosensitive Ca2+ channels (MCCs) mediates the Ca2+ wave propagation; an apoptotic cell shrinks accompanied by a Ca2+ transient, followed by pulling the edges of neighboring cells, which opens MCCs in neighboring cells, resulting in Ca2+ transients in these cells. Furthermore, Ca2+ wave propagation promotes Rac-Arp2/3 pathway-mediated polarized collective migration, generating approximately 1 kPa of force toward extruding cells. Our results uncovered a mechanochemical mechanism of Ca2+ wave propagation and its significant role in ACE.

DOI: https://doi.org/10.1038/s41467-025-65474-9
Nat Commun. 2025 Nov 20. 16(1): 10222

An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice.

Eloïse Marques, Stephen P Burr, Alva M Casey, Richard J Stopforth, Chak Shun Yu, Keira Turner, Dane M Wolf, Marisa Dilucca, Vincent Paupe, Suvagata Roy Chowdhury, Victoria J Tyrrell, Robbin Kramer, Yamini M Kanse, Chinmayi Pednekar, Chris A Powell, James B Stewart, Julien Prudent, Michael P Murphy, Michal Minczuk, Valerie B O'Donnell, Clare E Bryant, Patrick F Chinnery, Arthur Kaser, Alexander von Kriegsheim, Dylan G Ryan.

Impaired mitochondrial bioenergetics in macrophages promotes hyperinflammatory cytokine responses, but whether inherited mtDNA mutations drive similar phenotypes is unknown. Here, we profiled macrophages harbouring a heteroplasmic mitochondrial tRNAAla mutation (m.5019A>G) to address this question. These macrophages exhibit combined respiratory chain defects, reduced oxidative phosphorylation, disrupted cristae architecture, and compensatory metabolic adaptations in central carbon metabolism. Upon inflammatory activation, m.5019A>G macrophages produce elevated type I interferon (IFN), while exhibiting reduced pro-inflammatory cytokines and oxylipins. Mechanistically, suppression of pro-IL-1β and COX2 requires autocrine IFN-β signalling. IFN-β induction is biphasic: an early TLR4-IRF3 driven phase, and a later response involving mitochondrial nucleic acids and the cGAS-STING pathway. In vivo, lipopolysaccharide (LPS) challenge of m.5019A>G mice results in elevated type I IFN signalling and exacerbated sickness behaviour. These findings reveal that a pathogenic mtDNA mutation promotes an imbalanced innate immune response, which has potential implications for the progression of pathology in mtDNA disease patients.

DOI: https://doi.org/10.1038/s41467-025-65023-4
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2517961122

Longitudinal transformation of mitochondrial metabolism during neurogenesis.

Donghoon Lim, Sewon Park, Jong Seung Lee, Hyo Jin Gwon, Yunwoo Nam, Suhyuk Choi, Jongwon Kim, Yeonsu Kim, Geonwoo Park, Woo Yang Pyun, Hyun Woo Park, Seung-Woo Cho, Hyun S Ahn.

  Neural stem cells (NSCs) are valuable in the quest to conquer neurodegenerative diseases due to their capability to reconstruct the damaged neuronal networks. However, deep understanding of the intercellular signaling mechanism controlling the lineage and fate of the stem cells is required before potential clinical applications. Here, we applied nondestructive and label-free electrochemical methods for the longitudinal tracking of NSC respiratory metabolism. Sharp change in the oxygen utilization pattern was observed concomitant to stemness loss and onset of differentiation, suggesting metabolic reprogramming in the transition. Intra- and extracellular profiling of mitochondrial metabolites revealed molecular preference in the extracellular transport rates. Electrochemical emulation of the metabolite release pattern induced acceleration of neurite growth in nearby cells, suggesting paracrine signaling system mediated by mitochondrial metabolites.

Keywords:  intercellular signaling; neurogenesis; reactive oxygen species; scanning electrochemical microscopy

DOI:  https://doi.org/10.1073/pnas.2517961122
bioRxiv. 2025 Oct 02. pii: 2025.10.01.679790. [Epub ahead of print]

Traumatic brain injury exacerbates mitochondrial dysfunction in APP/PS1 knock-in mice through time-dependent pathways.

Elika Z Moallem, Hemendra J Vekaria, Teresa Macheda, Margaret R Hawkins, Kelly N Roberts, Samir P Patel, Patrick G Sullivan, Adam D Bachstetter.

  Cerebral hypometabolism occurs in both traumatic brain injury (TBI) and Alzheimer's disease (AD), but whether these conditions act through distinct or overlapping mechanisms is unclear. TBI disrupts cerebral metabolism via blood-brain barrier damage, altered glucose transporter expression, calcium buffering abnormalities, and oxidative damage to metabolic enzymes. AD-related hypometabolism is linked to amyloid-β (Aβ) effects on mitochondria, including impaired respiration, oxidative stress, and altered mitophagy, fusion, and fission. We tested whether TBI-induced mitochondrial dysfunction exacerbates Aβ-mediated impairment using a closed-head injury (CHI) model in APP/PS1 knock-in (KI) mice. Injuries were delivered at 4-5 months of age, before plaque formation and mitochondrial deficits in KI mice. Bioenergetics were measured at 1, 4, and 8 months post-injury in hippocampus and cortex using Seahorse assays on isolated mitochondria. At 1 month, genotype-by-injury interactions revealed greater dysfunction in KI mice than either condition alone, with males more vulnerable than females. At 4-8 months, amyloid-mediated effects predominated, while TBI-specific changes were no longer apparent, suggesting recovery or convergence onto shared mechanisms. These results indicate that TBI can temporarily worsen mitochondrial dysfunction in the context of early amyloidosis, with sex influencing vulnerability. Findings provide insight into the temporal relationship between TBI and amyloid-induced mitochondrial deficits and support the importance of sex as a biological variable in neurodegenerative disease progression.

Keywords:  Amyloid; Bioenergetics; Neurodegeneration; Neurotrauma; Sex differences

DOI:  https://doi.org/10.1101/2025.10.01.679790
J Clin Invest. 2025 Nov 17. pii: e193370. [Epub ahead of print]135(22):

Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.

Jie Zhao, Xinghao Li, Xinyu Li, Pengfei Ren, Yilan Wu, Hao Gong, Lijian Wu, Junran Huang, Saisai Wang, Ziwei Guo, Mo Chen, Zexian Zeng, Deng Pan.

  Macrophage-mediated phagocytosis plays a critical role in the elimination of cancer cells and shaping antitumor immunity. However, the tumor-intrinsic pathways that regulate cancer cell sensitivity to macrophage-mediated phagocytosis remain poorly defined. In this study, we performed a genome-wide CRISPR screen in murine pancreatic cancer cells cocultured with primary macrophages and identified that disruption of the tumor-intrinsic pyrimidine synthesis pathway enhances phagocytosis. Mechanistically, we discovered that macrophages inhibit the pyrimidine salvage pathway in tumor cells by upregulating Upp1-mediated uridine degradation through cytokines TNF-α and IL-1. This shift increased tumor cells' reliance on de novo pyrimidine synthesis. As a result, tumor cells with impaired de novo pyrimidine synthesis showed depleted UMP and displayed enhanced exposure of phosphatidylserine (PtdSer), a major "eat-me" signal, thereby promoting macrophage-mediated phagocytosis. In multiple pancreatic cancer models, Cad-deficient tumors exhibited markedly reduced tumor burden with increased levels of phagocytosis by macrophages. Importantly, the Cad-mediated suppression of pancreatic cancer was dependent on TAMs and cytokines IL-1 and TNF-α. Pharmacological inhibition of DHODH, which blocks de novo pyrimidine synthesis, similarly decreased tumor burden with enhanced phagocytosis in pancreatic cancer models. These findings highlight the critical role of the tumor-intrinsic pyrimidine synthesis pathway in modulating macrophage-mediated antitumor immunity, with potential therapeutic implications.

Keywords:  Cancer immunotherapy; Immunology; Innate immunity; Macrophages; Metabolism; Oncology

DOI:  https://doi.org/10.1172/JCI193370
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2505046122

Amyloid-beta glycation induces neuronal mitochondrial dysfunction and Alzheimer's pathogenesis via VDAC1-dependent mtDNA efflux.

Firoz Akhter, Asma Akhter, Xiongwei Zhu, Hillary Schiff, Arianna Maffei, Justin T Douglas, Qifa Zhou, Zhen Zhao, Donghui Zhu.

  Glycation, the nonenzymatic attachment of reactive dicarbonyls to proteins, lipids, or nucleic acids, contributes to the formation of advanced glycation end-products (AGEs). In Alzheimer's disease (AD), amyloid-beta (Aβ) undergoes posttranslational glycation to produce glycated Aβ (gAβ), yet its pathological role remains poorly understood. Here, we demonstrate that gAβ promotes neuronal mitochondrial DNA (mtDNA) efflux via a VDAC1-dependent mechanism, activating the innate immune cGAS-STING pathway. Using aged AD mice and human AD brain samples, we observed cGAS-mtDNA binding and cGAS-STING activation in the neuronal cytoplasm. Knockdown of RAGE, cGAS, or STING, as well as pharmacological inhibition of VDAC1, protected APP mice from mitochondrial dysfunction and Alzheimer's-like pathology. Neuron-specific cGAS knockdown confirmed its pivotal role in driving neuroinflammation and cognitive deficits. Treatment with ALT-711, an AGE cross-link breaker, alleviated gAβ-associated pathology. Furthermore, RAGE inhibition in APP knock-in mice suppressed innate immune activation and disease-associated gene expression, as revealed by spatially resolved transcriptomics. Collectively, our findings establish a mechanistic link between gAβ and innate immune activation, identifying VDAC1, the AGE-RAGE axis, and the cGAS-STING pathway as promising therapeutic targets in AD.

Keywords:  Alzheimer’s disease; glycated amyloid-beta; innate immunity; mitochondrial DNA

DOI:  https://doi.org/10.1073/pnas.2505046122
Nat Commun. 2025 Nov 17. 16(1): 10064

Structures of human organellar SPFH protein complexes.

Jingjing Gao, Dawafuti Sherpa, Nikita Kupko, Haruka Chino, Jianwei Zeng, Sichen Shao.

Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric rings that form domed structures. Most SPFH assemblies also abut a cellular membrane, where they are implicated in diverse functions ranging from membrane organization to protein quality control. However, the precise architectures of different SPFH complexes remain unclear. Here, we report single-particle cryo-EM structures of the endoplasmic reticulum (ER)-resident Erlin1/2 complex and the mitochondrial prohibitin (PHB1/2) complex, revealing assemblies of 13 heterodimers of Erlin1 and Erlin2 and 11 heterodimers of PHB1 and PHB2, respectively. We also describe key interactions underlying the architecture of each complex and conformational heterogeneity of the PHB1/2 complex. Our findings elucidate the distinct stoichiometries and properties of human organellar SPFH complexes and highlight common principles of SPFH complex organization.

DOI: https://doi.org/10.1038/s41467-025-65078-3
bioRxiv. 2025 Oct 01. pii: 2025.09.29.679307. [Epub ahead of print]

Retrograde mitochondrial transport regulates mitochondrial biogenesis in zebrafish neurons.

Angelica E Lang, Chris Stein, Catherine M Drerup.

To maintain a healthy mitochondrial population in a long-lived cell like a neuron, mitochondria must be continuously replenished through the process of mitochondrial biogenesis. Because the majority of mitochondrial proteins are nuclear encoded, mitochondrial biogenesis requires nuclear sensing of mitochondrial population health and function. This can be a challenge in a large, compartmentalized cell like a neuron in which a large portion of the mitochondrial population is in neuronal compartments far from the nucleus. Using in vivo assessments of mitochondrial biogenesis in zebrafish neurons, we determined that mitochondrial transport between distal axonal compartments and the cell body is required for sustained mitochondrial biogenesis. Estrogen-related receptor transcriptional activation links transport with mitochondrial gene expression. Together, our data support a role for retrograde feedback between axonal mitochondria and the nucleus for regulation of mitochondrial biogenesis in neurons.

DOI: https://doi.org/10.1101/2025.09.29.679307
Nat Commun. 2025 Nov 18. 16(1): 10047

Stable intracranial imaging of dura mater-engrafted pancreatic islet cells in awake mice.

Philip Tröster, Montse Visa, Ismael Valladolid-Acebes, Martin Köhler, Per-Olof Berggren.

By transplanting pancreatic islets onto the dura mater of the mouse brain, we establish a microscopy platform that enables longitudinal intravital imaging of otherwise optically inaccessible tissue. The system combines a cranial window with an air-cushioned floating arena and stable head fixation, providing high mechanical stability for repeated single-cell Ca2+ imaging sessions of up to 90 min in awake mice. We show that dura mater-engrafted islets integrate with host vascular and neural networks, and that human islet grafts secrete C-peptide in response to glucose stimulation, indicating metabolic integration. With this platform, we monitor anesthesia-induced changes in capillary blood flow and islet Ca2+ dynamics. In awake mice, following subcutaneous glucose injection, we characterize intracellular Ca2+ oscillations in insulin-secreting β-cells, revealing changes in amplitude, period, and plateau fraction while network coordination remains stable. The dura mater thus offers long-term optical access to functional endocrine tissue, facilitating stable intravital imaging under anesthesia-free, physiological conditions.

DOI: https://doi.org/10.1038/s41467-025-66057-4
EMBO Rep. 2025 Nov 20.

FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.

Suzan Ber, Ming Yang, Marco Sciacovelli, Shamith Samarajiwa, Khushali Patel, Efterpi Nikitopoulou, Annie Howitt, Simon J Cook, Ashok R Venkitaraman, Christian Frezza, Alessandro Esposito.

  Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.

Keywords:  Colorectal Cancer; FOXO Signalling; Glutamine Metabolism; Glutamine Synthase; KRAS Mutation

DOI:  https://doi.org/10.1038/s44319-025-00641-z
Sci Rep. 2025 Nov 21. 15(1): 41354

Resveratrol delays senescence of human dental pulp stem cells via activating the SIRT1-mitochondrial autophagy.

Zelu Li, Xiaoyang Chu, Jiahao Guo, Yulan Xiang, Yingyi Luan, Hongcheng Xing, Xixi Lv, Yanhong Zhou, Kai Yang, Yang Zeng, Dongliang Zhang.

  Human dental pulp stem cells (hDPSCs) senescence impairs their proliferation and osteogenic differentiation, critical for dental stem cell therapy. This study evaluated the effects of Resveratrol on the senescence of hDPSCs to explore new therapeutic strategies. Metabolomic analysis identified age-related metabolic differences in dental pulp tissues, with enriched pathways linked to Resveratrol. In vitro, Resveratrol improved proliferation, delayed senescence, promoted osteogenic differentiation, and enhanced mitochondrial autophagy, function, and biogenesis in senescent hDPSCs, reducing mitochondrial damage and oxidative stress. Mechanistically, silencing PINK1 or PGC-1α reversed Resveratrol-mediated promotion of proliferation, osteogenesis, and senescence suppression. Blocking SIRT1 abrogated its effects on mitochondrial quality control. These findings highlight Resveratrol's potential to mitigate hDPSCs senescence via SIRT1-dependent mitochondrial regulation, offering insights for age-related dental regenerative therapies.

Keywords:  PINK1 and PGC-1α; Resveratrol; SIRT1; Senescence; hDPSCs

DOI:  https://doi.org/10.1038/s41598-025-25240-9
Sci Rep. 2025 Nov 17. 15(1): 40201

Caloric restriction enhances inheritance of wild-type mitochondrial DNA in Saccharomyces cerevisiae.

Wenjuan Zhu, Minoru Yoshida, Feng Ling.

  In Saccharomyces cerevisiae, an asymmetrical division model, mitochondrial (mt) DNA typically exists in a homoplasmic state, but mutations frequently occur. Rolling-circle replication, mediated by the mtDNA recombinase Mhr1p, forms tandem concatemers that are selectively transmitted to budding cells. In crosses between haploids with wild-type (ρ+) and hypersuppressive (HS) ρ- mtDNA, ρ- progeny are predominantly produced due to the replicative advantage of mtDNA with large deletions. We investigated the effects of caloric restriction (CR; 0.5% glucose medium) on mitochondrial distribution and found that ρ+ mtDNA-mitochondria are pre-selected in zygotes and transmitted into buds prior to mitochondrial fusion. This process, termed ρ+ mtDNA-mitochondrial preselection and transmission (ρ+ mtDNA-MPT), was validated by confocal imaging and flow cytometry analyses. The rate of ρ+ progeny increased under CR conditions compared to glucose-abundant media, suggesting that CR enhances ρ+ mtDNA-MPT and promotes the formation of wild-type mtDNA homoplasmy via an Mhr1p-dependent mechanism, which dominates mtDNA inheritance.

Keywords:  Heteroplasmy; Homoplasmy; Hypersuppresiveness; Mitochondria; Nonmedial budding.; Preselection; mtDNA

DOI:  https://doi.org/10.1038/s41598-025-23888-x